RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16767
(1020 letters)
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 5, represents the discontinuous cleft
domain that is required to from the central cleft or
channel where the DNA is bound.
Length = 447
Score = 255 bits (654), Expect = 1e-75
Identities = 105/361 (29%), Positives = 146/361 (40%), Gaps = 72/361 (19%)
Query: 361 GIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQV 420
G+ PQEFFFH M GREGLIDTAVKT+ +GYLQR LVK LE L V YD TVR+S ++Q
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQF 60
Query: 421 LYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKHPLSLALLLLLTFKSSGK 480
LYGEDGLD K + + ++ K L L L+ L T
Sbjct: 61 LYGEDGLDPLKIEGQGRFTIEDSDLKLE-----KKFKIDLNDVLLLLSEFSLSTLL---- 111
Query: 481 PNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENLA 540
+++ ++ +
Sbjct: 112 --------------------FEILLRSGIE------------------------------ 121
Query: 541 DSVVKYTKGRTDASHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHF 600
S ++ ++ F K SL PGE VG++AAQSIGEP TQMTLNTFHF
Sbjct: 122 -SKRVRSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHF 180
Query: 601 AGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKAN-RLAKSMTRITMA 659
AG NVTLG+PRL+EI+ +A K + + + R K++ +
Sbjct: 181 AGVASKNVTLGVPRLKEIINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLL--- 237
Query: 660 DVLEKVKIKEWLEISPEPHMNYQ-----MKFCFIPAHMYRDKTSVKPSKIIDHFERKFLK 714
+KV I + + + + II + + K
Sbjct: 238 ---KKVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRKRK 294
Query: 715 E 715
+
Sbjct: 295 K 295
Score = 114 bits (287), Expect = 1e-26
Identities = 53/220 (24%), Positives = 88/220 (40%), Gaps = 25/220 (11%)
Query: 759 LGRVDVSSDEE-RDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKI 817
L V+ ++D+ + K ++ + +E EE I + K
Sbjct: 235 LLLKKVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPEEVA----EEVALAIIIIGKRKS 290
Query: 818 EFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPSNLFEEKESKH---------- 867
R N+ V + + + ++ + +
Sbjct: 291 RKRKKNNLGVAKDE--KGLEEEELLLLNKIL--LVIPGIKVKYGVILTDGRVDPHTILEK 346
Query: 868 -----LLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAV 922
LLKT+G N+ + + + ++D +K Y NDI M GIEAA I+ E++NVF
Sbjct: 347 LGKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKF 406
Query: 923 YGIEVDPRHLSLVADYMTHSGTYVAMNRNGI-RLNPSFIQ 961
GI V+ RHL+L+AD MT G + + R G+ R SFI
Sbjct: 407 DGIYVNRRHLALLADLMTFKGELLGITRAGLNREKSSFIL 446
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 249 bits (639), Expect = 1e-69
Identities = 141/428 (32%), Positives = 210/428 (49%), Gaps = 50/428 (11%)
Query: 13 KAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAK-LSLRDTFLTRAEYMNLVYQALCI 71
+AEA LM V L P+ G P+ G IQDH ISGA L+ + T T+ E ++L+ A
Sbjct: 474 RAEARILMLVQEHILSPRYGGPIIGGIQDH-ISGAYLLTRKSTLFTKEEALDLLRAA--- 529
Query: 72 LNTEIRTLP---PTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGS 128
I LP P I P WTGKQ+ S PKD + ++ SG + K+
Sbjct: 530 ---GIDELPEPEPAIENGKPYWTGKQIFSL----FLPKDLNLEFKAKICSGCDECKK--- 579
Query: 129 TQYGLVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAK 188
D +V I++G+LL G++DKK G+ Q ++ + +G E A L + +
Sbjct: 580 -----EDCEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTR 634
Query: 189 LFTVYLQRVGFTLGVRDILVRQERDRKRTKIIN----KARRLGTEAACNAL-GLPLDTDP 243
L ++ GFT G+ D + +E + +II + L L LP T
Sbjct: 635 LAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLE 694
Query: 244 EIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVES 303
E + ++ + +L K + ++ E + N M +
Sbjct: 695 ETLEMKIMQ------------------VLGKARDEAGEIA--EKYLGLD--NPAVIMART 732
Query: 304 GAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQ 363
GA+GS +N Q++ +GQ + G+R RTLP F P ++ A GFV + +G+
Sbjct: 733 GARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLT 792
Query: 364 PQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYG 423
P EFFFH M GREGL+DTAV+TS+SGY+QR L+ L+ L V YD TVRD+ +++Q YG
Sbjct: 793 PTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYG 852
Query: 424 EDGLDVTK 431
EDG+D K
Sbjct: 853 EDGVDPMK 860
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 251 bits (641), Expect = 1e-68
Identities = 167/674 (24%), Positives = 270/674 (40%), Gaps = 101/674 (14%)
Query: 13 KAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCIL 72
+AEA LM V + P+ G P+ G +QD + + ++ D + E N+ A
Sbjct: 490 RAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGI-- 547
Query: 73 NTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYG 132
T+ P K P WTGKQ+ S PKD GI + +
Sbjct: 548 -TDPLPEPAIKTKDGPAWTGKQLFSL----FLPKDFNFE-------GIAKWSAGKAGEAK 595
Query: 133 LVHAVWDTHVTIRHGELLSGILDKKQFGSTQYG---LVHAVWDTHGAEHAISLLSCLAKL 189
+ D +V I+ GEL+SG++D G+ L+ + +G AI L+ + +
Sbjct: 596 DPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKILII 655
Query: 190 FTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQ 249
+ GF+ G D+++ E ++ I + ++ + I +
Sbjct: 656 AKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQ---RKITRKITIYKGK 712
Query: 250 LQEAYASIPQ--FRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKG 307
+ + A I + DK ++ N C+ N + M ++GA+G
Sbjct: 713 EELLRGMKEEEALEADIVNELDKARDKAGSSAND-CID-------ADNAGKIMAKTGARG 764
Query: 308 STVNTMQISCLLGQ--------IELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFM 359
S N QI+ LGQ L G R R L F + +P A GFV +
Sbjct: 765 SMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYR 824
Query: 360 TGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQ 419
G+ EFFFH M GREGLID A +T SGY QR L LE + + YD TVRD +IQ
Sbjct: 825 EGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQ 884
Query: 420 VLYGEDGLDVTKRQYLTDKQFSFLEDNIKWICSYKVILNLLKKHPLSLALLLLLTFKSSG 479
+GEDG+ D Q
Sbjct: 885 FKFGEDGI---------DPQKLD------------------------------------- 898
Query: 480 KPNFIFSPHRTKFTMDLLEQWYQLDDKARKKYRKKFKACPQPLISTFQPDAHFGSISENL 539
H F ++ + + +++D+ + + + + + TF + + + L
Sbjct: 899 --------HGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNAN-----LPKLL 945
Query: 540 ADSVVKYTKGRTDASHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFH 599
AD++ + + F K + PG+ +G+++AQSI EP TQMTL TFH
Sbjct: 946 ADAIHGAELKEDELEAICAEGKEGFEK---AKVEPGQAIGIISAQSIAEPGTQMTLRTFH 1002
Query: 600 FAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMA 659
AG M+VT G+ R E L+ A TP+M+I + + +KA +A+++ + +
Sbjct: 1003 AAGIKAMDVTHGLERFIE-LVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVR 1061
Query: 660 DVLEKVKIKEWLEI 673
++ I EI
Sbjct: 1062 ALIADSAIDNANEI 1075
Score = 70.1 bits (171), Expect = 5e-12
Identities = 41/156 (26%), Positives = 71/156 (45%), Gaps = 8/156 (5%)
Query: 866 KHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 925
+ +++T G N+ + + + +D+ ND +A T GIEAA I E+ ++ G+
Sbjct: 1167 EWIIQTSGSNLAAVLEMK-CIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
Query: 926 EVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSF-------IQKMTFEMPLEKIRQASMQ 978
EVD R++ LVAD M GT A+ + F + K FE+ I A++
Sbjct: 1226 EVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALG 1285
Query: 979 GREDSLRAPSARVMLGQECRQGTGLFQLRNREKKKK 1014
G + ++ +++GQ G+G L K
Sbjct: 1286 GEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 246 bits (629), Expect = 2e-68
Identities = 135/424 (31%), Positives = 206/424 (48%), Gaps = 38/424 (8%)
Query: 13 KAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCIL 72
+AEA LM V L P+ G P+ G I D++ L+ + T T+ E V L +
Sbjct: 470 RAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEE----VQTILGVA 525
Query: 73 NTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYG 132
P I KP WTGKQ+ S + P+D ++ S KK+
Sbjct: 526 GYFGDPPEPAIEKPKEYWTGKQIFSAFL----PEDLNFEGRAKICSSDACKKEECPH--- 578
Query: 133 LVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTV 192
D +V I++G+LL G++DKK G+ + ++H + +G E A L + +LF
Sbjct: 579 ------DAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIR 632
Query: 193 YLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQE 252
++ GFT G+ DI + +E + ++I KA E + +I
Sbjct: 633 FITLRGFTTGIDDIDIPKEAKEEIEELIEKA-----EKRVD----------NLIERYRNG 677
Query: 253 AYASIPQFRAQIDRQYK--SLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTV 310
+P + + K +L K + +V E ++P N+ M +GA+GS +
Sbjct: 678 ELEPLPGRTVEETLEMKIMEVLGKARDEAGEVA--EKYLDPE--NHAVIMARTGARGSLL 733
Query: 311 NTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFH 370
N Q++ ++GQ + G R RTLP F ++ +A GFV F G+ P E+FFH
Sbjct: 734 NITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFH 793
Query: 371 CMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVT 430
GREGL+DTAV+TS+SGY+QR L+ L+ L V YD TVRD+ +LIQ YGEDG+D
Sbjct: 794 AAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPM 853
Query: 431 KRQY 434
K +
Sbjct: 854 KSDH 857
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 233 bits (596), Expect = 2e-64
Identities = 110/425 (25%), Positives = 169/425 (39%), Gaps = 51/425 (12%)
Query: 14 AEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILN 73
AEA LM L P G P+ IQD V L++ D L + +
Sbjct: 422 AEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEY--- 478
Query: 74 TEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSG-ILDKKQFGSTQYG 132
+ R I K + L TGK ++ST+ +L ++ G + L + +
Sbjct: 479 ADDREKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDGRRIFNRGLPEDK------- 531
Query: 133 LVHAVWDTHVTIRHGELLSGILDKKQFGSTQ-YGLVHAVWDTHGAEHAISLLSCLAKLFT 191
D V I +G+L+ G++DKK + YG A + LL L L
Sbjct: 532 ------DVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKAL------VKLLDKLKNLGI 579
Query: 192 VYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQ 251
+ G +G +DI E+D +I+ +A + ++I Q +
Sbjct: 580 KGIGGFGIGIGRKDIEAEDEKD----EIVIEAE---------------GSVLKLIL-QYE 619
Query: 252 EAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVN 311
E + R I + L + N + L E + G G+ +N
Sbjct: 620 EGDLT-RTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVD--IRHMGLSGARMN 676
Query: 312 TMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHC 371
QI L+GQ + G++ +S +F A G + F+ G+ E+F H
Sbjct: 677 ISQIVQLIGQQGVMGEK----ISVLARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHP 732
Query: 372 MAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLDVTK 431
+ GR GL+DTA+KT+ SGYL R LV + L V D V D +IQ YGEDG D+T+
Sbjct: 733 IGGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDCVTDGIGVVIQFEYGEDGEDLTE 792
Query: 432 RQYLT 436
R
Sbjct: 793 RILGR 797
Score = 69.6 bits (171), Expect = 5e-12
Identities = 59/267 (22%), Positives = 104/267 (38%), Gaps = 29/267 (10%)
Query: 548 KGRTDASH--VDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAG--R 603
+G+ H V + Y+ F + +A G AA++ G TQM + T H+ G
Sbjct: 387 EGKAIRLHPLVCEAYNADFDGD--EMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIV 444
Query: 604 GDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLE 663
+ T+G P L I+ K TP EI + +KA +AK + T
Sbjct: 445 APIQDTVGGPYLLTIV--DAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTT-----G 497
Query: 664 KVKIKEWLEISPEPHMNYQMKFCFIPAHMYRDKTSVKPSKIIDH-FERKFLKELEVAIAK 722
KV + E + I + V KI++ + + + V I +
Sbjct: 498 KVIVSTISPDLAELSIIVTTDGRRIFNRGLPEDKDV-LVKIVNGKLIKGVIDKKIVTIYR 556
Query: 723 RAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDE-----EDAVQ 777
+ + + + D++++ +G G G +GR D+ +++E+DE E +V
Sbjct: 557 EYGPEVASKALVKLLDKLKNLGI----KGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVL 612
Query: 778 SHKKVNQEEDNDFEEPEDEERMSEREE 804
K + Q E+ D ER + E
Sbjct: 613 --KLILQYEEGD---LTRTERNNIVEI 634
Score = 42.2 bits (100), Expect = 0.001
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 861 EEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 920
E+++ + +++ +G + I QY DL + N+I + GIEA II E+K
Sbjct: 597 EDEKDEIVIEAEGSVLKLILQYEEG-DLTRTERNNIVEIIEVLGIEALRNAIIEEIKITL 655
Query: 921 AVYGIE-VDPRHLSLVADYMTHSGT 944
G++ VD RH+ L M S
Sbjct: 656 EEQGLDFVDIRHMGLSGARMNISQI 680
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA
polymerase II (RNAP II), C-terminal domain. RNA
polymerase II (RNAP II) is a large multi-subunit complex
responsible for the synthesis of mRNA. RNAP II consists
of a 10-subunit core enzyme and a peripheral heterodimer
of two subunits. The largest core subunit (Rpb1) of yeast
RNAP II is the best characterized member of this family.
Structure studies suggest that RNAP complexes from
different organisms share a crab-claw-shape structure. In
yeast, Rpb1 and Rpb2, the largest and the second largest
subunits, each makes up one clamp, one jaw, and part of
the cleft. Rpb1 interacts with Rpb2 to form the DNA entry
and RNA exit channels in addition to the catalytic center
of RNA synthesis. The C-terminal domain of Rpb1 makes up
part of the foot and jaw structures.
Length = 410
Score = 216 bits (552), Expect = 7e-62
Identities = 128/450 (28%), Positives = 214/450 (47%), Gaps = 66/450 (14%)
Query: 563 IFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMA 622
F + SL +PGE VG +AAQSIGEP+TQMTLNTFHFAG NVTLG+PRL+EI+
Sbjct: 18 RFNR---SLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NV 73
Query: 623 TKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHMNYQ 682
K IKTPS+ + P K E+KA ++ + T+ DV +I + + P+P
Sbjct: 74 AKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEI--YYD--PDP----- 124
Query: 683 MKFCFIPAHMYRDKTSVKPSKII--DHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQM 740
T ++ K +FE F E +V + + L+ IE R +M
Sbjct: 125 ------------QNTVIEEDKEFVESYFE--FPDE-DVEQDRLSPWLLR---IELDRKKM 166
Query: 741 ED---DVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEE 797
D +E + E L +V ++ E+ + ++ +++ + EE +++
Sbjct: 167 TDKKLSMEQIAKKIKEEFKDDL---NVIFSDDNAEKLVI--RIRIINDDE-EKEEDSEDD 220
Query: 798 RMSEREEDDNTSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPS 857
++ E + S++ + K + + N +
Sbjct: 221 VFLKKIESNMLSDMTLK-------GIEGIRKVFIREENKKKVDIETGE------------ 261
Query: 858 NLFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVK 917
+K + +L+TDG+N+ + + +D + NDI + GIEAA + +++E++
Sbjct: 262 ---FKKREEWVLETDGVNLREVLSHPG-VDPTRTTSNDIVEIFEVLGIEAARKALLKELR 317
Query: 918 NVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGI-RLNPSFIQKMTFEMPLEKIRQAS 976
NV + G V+ RHL+L+ D MT G +A+ R+GI R + + + +FE ++ + +A+
Sbjct: 318 NVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAA 377
Query: 977 MQGREDSLRAPSARVMLGQECRQGTGLFQL 1006
G D L+ S +MLGQ GTG F L
Sbjct: 378 AFGETDDLKGVSENIMLGQLAPIGTGCFDL 407
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA polymerase
I (RNAP I) is a multi-subunit protein complex responsible
for the synthesis of rRNA precursor. It consists of at
least 14 different subunits, and the largest one is
homologous to subunit Rpb1 of yeast RNAP II and subunit
beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in
yeast. Structure studies suggest that different RNAP
complexes share a similar crab-claw-shape structure. The
C-terminal domain of Rpb1, the largest subunit of RNAP
II, makes up part of the foot and jaw structures of RNAP
II. The similarity between this domain and the C-terminal
domain of Rpb1, its counterpart in RNAP II, suggests a
similar functional and structural role.
Length = 309
Score = 212 bits (543), Expect = 8e-62
Identities = 70/147 (47%), Positives = 106/147 (72%)
Query: 861 EEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 920
+ ++K+L+ T+G+N+ + ++ +LD+N++Y NDIH M +TYGIEAA R I++E+ NVF
Sbjct: 163 KGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVF 222
Query: 921 AVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSFIQKMTFEMPLEKIRQASMQGR 980
VYGI VDPRHLSL+ADYMT G Y NR G+ + S +QKM+FE L +++A++ G
Sbjct: 223 KVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESSTSPLQKMSFETTLAFLKKATLNGD 282
Query: 981 EDSLRAPSARVMLGQECRQGTGLFQLR 1007
D+L +PS+R+++G+ GTGLF L
Sbjct: 283 IDNLSSPSSRLVVGKPVNGGTGLFDLL 309
Score = 193 bits (493), Expect = 5e-55
Identities = 68/107 (63%), Positives = 84/107 (78%), Gaps = 2/107 (1%)
Query: 566 KNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKA 625
K + SL PGE VG+LAAQSIGEPSTQMTLNTFHFAGRG+MNVTLGIPRLREILM A+K
Sbjct: 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKN 60
Query: 626 IKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLE 672
IKTPSM +P ++A L K ++R+T++DV+EKV++ E L+
Sbjct: 61 IKTPSMTLPLKNGKSA--ERAETLKKRLSRVTLSDVVEKVEVTEILK 105
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 138 bits (349), Expect = 1e-37
Identities = 62/184 (33%), Positives = 88/184 (47%), Gaps = 28/184 (15%)
Query: 25 QYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILNTEIRTLPPTIW 84
L P++G P+ G QD V+ L+ RDTF R E M L+ I P I
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYG-------IVLPHPAIL 53
Query: 85 KPM-PLWTGKQVLSTVIIN-LTPKDKVIIRHGELLSGILDKKQFGSTQYGLVHAVWDTHV 142
KP+ PLWTGKQ S ++ N + PK K L D++V
Sbjct: 54 KPIKPLWTGKQTFSRLLPNEINPKGKPKTNEETLCEN-------------------DSYV 94
Query: 143 TIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLG 202
I +GEL+SG++DKK G + L+H ++ +G E + L L KL YL + GF++G
Sbjct: 95 LINNGELISGVIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSIG 154
Query: 203 VRDI 206
+ DI
Sbjct: 155 IDDI 158
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 114 bits (287), Expect = 3e-27
Identities = 55/134 (41%), Positives = 80/134 (59%), Gaps = 3/134 (2%)
Query: 534 SISENLADSVVKYTKGRTDASHVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQM 593
+ + L ++V K +D +D+ + + L SL +PGE VG++AAQSIGEP TQM
Sbjct: 5 KLLKELEETVKKR--EISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQM 62
Query: 594 TLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSM 653
T+ TFH+AG ++NVTLG+PRL EI+ A K TPSM I + K +KA +AK +
Sbjct: 63 TMRTFHYAGVAELNVTLGLPRLIEIV-DARKTPSTPSMTIYLEDEYEKDREKAEEVAKKI 121
Query: 654 TRITMADVLEKVKI 667
+ DV + + I
Sbjct: 122 EATKLEDVAKDISI 135
Score = 94.3 bits (235), Expect = 2e-20
Identities = 47/147 (31%), Positives = 77/147 (52%), Gaps = 2/147 (1%)
Query: 862 EKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 921
++ ++++ T+G N+ + + + D + NDIH +A GIEAA II E+K
Sbjct: 220 KEGDEYVIYTEGSNLKEVLKLEGV-DKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLE 278
Query: 922 VYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLN-PSFIQKMTFEMPLEKIRQASMQGR 980
G++VD RHL LVAD MT G + R+GI S + + FE+ ++ + A+++G
Sbjct: 279 EQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGE 338
Query: 981 EDSLRAPSARVMLGQECRQGTGLFQLR 1007
D L +++GQ GTG L
Sbjct: 339 VDELAGVIENIIVGQPIPLGTGDVDLV 365
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is
a large multi-subunit complex responsible for the
synthesis of all RNAs in the cell. The relative
positioning of the RNAP core is highly conserved between
archaeal RNAP and the three classes of eukaryotic RNAPs.
In archaea, the largest subunit is split into two
polypeptides, A' and A'', which are encoded by separate
genes in an operon. Sequence alignments reveal that the
archaeal A'' subunit corresponds to the C-terminal
one-third of the RNAPII largest subunit (Rpb1). In
subunit A'', several loops in the jaw domain are
shorter. The RNAPII Rpb1 interacts with the
second-largest subunit (Rpb2) to form the DNA entry and
RNA exit channels in addition to the catalytic center of
RNA synthesis.
Length = 363
Score = 113 bits (286), Expect = 5e-27
Identities = 47/98 (47%), Positives = 64/98 (65%), Gaps = 1/98 (1%)
Query: 570 SLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTP 629
SL PGE VG++AAQSIGEP TQMTL TFH+AG ++NVTLG+PRL EI+ A K TP
Sbjct: 35 SLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV-DARKEPSTP 93
Query: 630 SMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKI 667
+M I + +KA +A+ + T+ ++ E + I
Sbjct: 94 TMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI 131
Score = 96.6 bits (241), Expect = 2e-21
Identities = 43/122 (35%), Positives = 66/122 (54%), Gaps = 1/122 (0%)
Query: 887 DLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYV 946
D + N+IH + GIEAA II E+K G++VD RH+ LVAD MT+ G
Sbjct: 239 DPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVR 298
Query: 947 AMNRNGIR-LNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQ 1005
+ R+GI PS + + FE+ ++ + A+++G D LR +++GQ GTG +
Sbjct: 299 QIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVE 358
Query: 1006 LR 1007
L
Sbjct: 359 LT 360
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
polymerase III (RNAP III), C-terminal domain.
Eukaryotic RNA polymerase III (RNAP III) is a large
multi-subunit complex responsible for the synthesis of
tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is
also known as C160 in yeast. Structure studies suggest
that different RNA polymerase complexes share a similar
crab-claw-shape structure. The C-terminal domain of
Rpb1, the largest subunit of RNAP II, makes up part of
the foot and jaw structures of RNAP II. The similarity
between this domain and the C-terminal domain of Rpb1,
its counterpart in RNAP II, suggests a similar
functional and structural role.
Length = 300
Score = 111 bits (281), Expect = 5e-27
Identities = 43/102 (42%), Positives = 61/102 (59%), Gaps = 3/102 (2%)
Query: 566 KNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKA 625
K + + PG VG +AAQSIGEP TQMTL TFHFAG MN+TLG+PR++EI + A+K
Sbjct: 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEI-INASKN 59
Query: 626 IKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKI 667
I TP + D + EK A + + + + +V ++
Sbjct: 60 ISTPIITAKLEND--RDEKSARIVKGRIEKTYLGEVASYIEE 99
Score = 93.8 bits (234), Expect = 9e-21
Identities = 39/119 (32%), Positives = 64/119 (53%), Gaps = 1/119 (0%)
Query: 887 DLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYV 946
+ N I + GIEAA II E++ +G+ +DPRH+ L+AD MT G +
Sbjct: 182 IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVL 241
Query: 947 AMNRNGI-RLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLF 1004
+ R GI ++ S + +FE + + A++ GR+DS+ S +++G+ GTGLF
Sbjct: 242 GITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 112 bits (282), Expect = 2e-26
Identities = 45/98 (45%), Positives = 63/98 (64%), Gaps = 1/98 (1%)
Query: 570 SLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTP 629
SL PGE VGV+AAQSIGEP TQMT+ TFH+AG ++NVTLG+PRL EI + A K TP
Sbjct: 54 SLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEI-VDARKEPSTP 112
Query: 630 SMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKI 667
M I + +KA +A+ + T+ ++ + + +
Sbjct: 113 MMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV 150
Score = 89.9 bits (224), Expect = 6e-19
Identities = 48/158 (30%), Positives = 77/158 (48%), Gaps = 19/158 (12%)
Query: 857 SNLFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREV 916
SNL K +LK +G+ D + N+IH + GIEAA II E+
Sbjct: 244 SNL------KEVLKVEGV------------DATRTTTNNIHEIEEVLGIEAARNAIIEEI 285
Query: 917 KNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIR-LNPSFIQKMTFEMPLEKIRQA 975
KN G++VD RH+ LVAD MT G + R+G+ S + + FE+ ++ + A
Sbjct: 286 KNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDA 345
Query: 976 SMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREKKK 1013
+++G D L+ + +++GQ GTG +L +
Sbjct: 346 AVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPLR 383
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase
(RNAP), C-terminal domain. RNA polymerase (RNAP) is a
large multi-subunit complex responsible for the synthesis
of RNA. It is the principal enzyme of the transcription
process, and is the final target in many regulatory
pathways that control gene expression in all living
cells. At least three distinct RNAP complexes are found
in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for
the synthesis of ribosomal RNA precursor, mRNA precursor,
and 5S and tRNA, respectively. A single distinct RNAP
complex is found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. Structure
studies revealed that prokaryotic and eukaryotic RNAPs
share a conserved crab-claw-shape structure. The largest
and the second largest subunits each make up one clamp,
one jaw, and part of the cleft. The largest RNAP subunit
(Rpb1) interacts with the second-largest RNAP subunit
(Rpb2) to form the DNA entry and RNA exit channels in
addition to the catalytic center of RNA synthesis. The
region covered by this domain makes up part of the foot
and jaw structures. In archaea, some photosynthetic
organisms, and some organelles, this domain exists as a
separate subunit, while it forms the C-terminal region of
the RNAP largest subunit in eukaryotes and bacteria.
Length = 158
Score = 99.4 bits (248), Expect = 4e-24
Identities = 41/110 (37%), Positives = 59/110 (53%), Gaps = 1/110 (0%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNG-I 953
IH M GIEAA IIRE++ V A G+ VD RH+ L+AD MT+SG + R+G
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFR 108
Query: 954 RLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGL 1003
S + + +FE + + A+ G +D L S ++LG+ GTG
Sbjct: 109 ASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
Score = 93.3 bits (232), Expect = 6e-22
Identities = 38/48 (79%), Positives = 40/48 (83%)
Query: 575 GENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMA 622
GE VGVLAAQSIGEP TQMTL TFHFAG MNVTLG+PRL+EIL A
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 104 bits (260), Expect = 4e-23
Identities = 46/91 (50%), Positives = 60/91 (65%), Gaps = 1/91 (1%)
Query: 571 LANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPS 630
+P E VG++AAQSIGEP TQMT+ TFH+AG +MNVTLG+PRL EI + A K TP+
Sbjct: 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEI-VDARKKPSTPT 236
Query: 631 MEIPFLPDMPKLEKKANRLAKSMTRITMADV 661
M I D + E+K +AK + T+ DV
Sbjct: 237 MTIYLKKDYREDEEKVREVAKKIENTTLIDV 267
Score = 86.0 bits (213), Expect = 2e-17
Identities = 54/175 (30%), Positives = 80/175 (45%), Gaps = 20/175 (11%)
Query: 842 YDKKNHMWCKLLFLPSNLFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMAS 901
+ W + SNL K +L+ D + D + Y NDI +A+
Sbjct: 354 KENDERRW-VIYTQGSNL------KDVLEIDEV------------DPTRTYTNDIIEIAT 394
Query: 902 TYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIR-LNPSFI 960
GIEAA II E K G+ VD RH+ LVAD MT G+ A+ R+GI S +
Sbjct: 395 VLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVL 454
Query: 961 QKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLFQLRNREKKKKK 1015
+ FE+ + + +A + G D L + +++GQ GTG L + +KK K
Sbjct: 455 ARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRKKVK 509
>gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 4, represents the funnel domain. The
funnel contain the binding site for some elongation
factors.
Length = 108
Score = 93.6 bits (233), Expect = 1e-22
Identities = 31/86 (36%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 269 KSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKR 328
++L+K + + P N++ M +SGAKGS +N QI+ GQ +EGKR
Sbjct: 27 NNILNKARDPAGNIASKS----LDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGKR 82
Query: 329 PAMMVSGRTLPSFLPYEVSPRAGGFV 354
SGRTLP F + P + GFV
Sbjct: 83 IPFGFSGRTLPHFKKDDEGPESRGFV 108
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 75.3 bits (185), Expect = 1e-13
Identities = 44/134 (32%), Positives = 66/134 (49%), Gaps = 4/134 (2%)
Query: 886 LDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSGTY 945
+D ++ N+I + GIEAA II E+ N G+EVD RHL LVAD MT G
Sbjct: 725 VDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEV 784
Query: 946 VAMNRNGIRLNP-SFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGLF 1004
+ R+G+ S + + FE ++ + A+ G D L+ V++G+ + GTG
Sbjct: 785 KPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCV 844
Query: 1005 QL---RNREKKKKK 1015
L R E+ K
Sbjct: 845 DLRIDREYEEGKND 858
Score = 59.1 bits (143), Expect = 9e-09
Identities = 30/80 (37%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 591 TQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLA 650
T T+ TFH+AG ++NVTLG+PR+ EI+ A K TP M + + +KA +A
Sbjct: 541 THNTMRTFHYAGVAEINVTLGLPRMIEIV-DARKEPSTPIMTVHLKGEYATDREKAEEVA 599
Query: 651 KSMTRITMADVLEKVKIKEW 670
K + +T+ DV + I W
Sbjct: 600 KKIESLTLGDVATSIAIDLW 619
Score = 41.4 bits (97), Expect = 0.003
Identities = 19/31 (61%), Positives = 23/31 (74%), Gaps = 2/31 (6%)
Query: 565 YKNLLSLANPGENVGVLAAQSIGEPSTQMTL 595
Y N +L P E VG++AAQSIGEP TQM+L
Sbjct: 49 YLN--ALVEPYEAVGIVAAQSIGEPGTQMSL 77
>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial
DNA-dependent RNA polymerase (RNAP), C-terminal domain.
Bacterial RNA polymerase (RNAP) is a large multi-subunit
complex responsible for the synthesis of all RNAs in the
cell. This family also includes the eukaryotic
plastid-encoded RNAP beta" subunit. Structure studies
suggest that RNAP complexes from different organisms
share a crab-claw-shape structure with two pincers
defining a central cleft. Beta' and beta, the largest
and the second largest subunits of bacterial RNAP, each
makes up one pincer and part of the base of the cleft.
The C-terminal domain includes a G loop that forms part
of the floor of the downstream DNA-binding cavity. The
position of the G loop may determine the switch of the
bridge helix between flipped-out and normal
alpha-helical conformations.
Length = 204
Score = 66.8 bits (164), Expect = 2e-12
Identities = 26/51 (50%), Positives = 34/51 (66%), Gaps = 3/51 (5%)
Query: 570 SLANPGENVGVLAAQSIGEPSTQMTLNTFHFAG-RGDMNVTLGIPRLREIL 619
L GE VG++AAQSIGEP TQ+T+ TFH G D +T G+PR+ E+
Sbjct: 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVATD--ITQGLPRVEELF 49
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 63.9 bits (156), Expect = 3e-10
Identities = 27/53 (50%), Positives = 36/53 (67%), Gaps = 4/53 (7%)
Query: 570 SLANPGENVGVLAAQSIGEPSTQMTLNTFH---FAGRGDMNVTLGIPRLREIL 619
L GE VGV+AAQSIGEP TQ+T+ TFH AG ++T G+PR++E+
Sbjct: 866 KLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASG-DITQGLPRVKELF 917
Score = 53.5 bits (129), Expect = 6e-07
Identities = 66/272 (24%), Positives = 104/272 (38%), Gaps = 76/272 (27%)
Query: 154 LDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERD 213
L KK+ S L+ +++ HG E +L + L Y + G T+ DI+V E+
Sbjct: 565 LSKKEISS----LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKY 620
Query: 214 RKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQI---DRQYKS 270
EI+ +E + + + +Y+
Sbjct: 621 ------------------------------EILKEADKEVAKIQKFYNKGLITDEERYRK 650
Query: 271 LL-------DKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIE 323
++ DKVT+ + L + + + N + M +SGA+G+ Q
Sbjct: 651 VVSIWSETKDKVTDAM-MKLLKK---DTYKFNPIFMMADSGARGNISQFRQ--------- 697
Query: 324 LEGKRPAMM-VSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTA 382
L G R M SG + LP + S F G+ E+F R+GL DTA
Sbjct: 698 LAGMRGLMAKPSGDIIE--LPIKSS----------FREGLTVLEYFISTHGARKGLADTA 745
Query: 383 VKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSD 414
+KT+ SGYL R LV V D+ VR+ D
Sbjct: 746 LKTADSGYLTRRLVD------VAQDVVVREED 771
Score = 31.9 bits (73), Expect = 2.0
Identities = 29/148 (19%), Positives = 56/148 (37%), Gaps = 39/148 (26%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT-------------- 940
D H + GI+A +++EV+ V+ + G+E++ +H+ ++ M
Sbjct: 988 DPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLL 1047
Query: 941 -----HSGTYVAMNRN----------------GIRLNP----SFIQKMTFEMPLEKIRQA 975
+ NR GI SF+ +F+ + + A
Sbjct: 1048 PGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDA 1107
Query: 976 SMQGREDSLRAPSARVMLGQECRQGTGL 1003
+++G+ D L V++G GTGL
Sbjct: 1108 AIKGKVDYLLGLKENVIIGNLIPAGTGL 1135
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 63.2 bits (155), Expect = 6e-10
Identities = 27/48 (56%), Positives = 36/48 (75%), Gaps = 3/48 (6%)
Query: 571 LANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREI 618
L N GE VGV+AAQSIGEP TQ+T+ TFH G +++T G+PR+ E+
Sbjct: 875 LVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGG---VDITGGLPRVAEL 919
Score = 38.9 bits (92), Expect = 0.015
Identities = 34/104 (32%), Positives = 47/104 (45%), Gaps = 24/104 (23%)
Query: 295 NNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMV--SGRTLPSFLPYEVSPRAGG 352
N + M +SGA+G + QI +L G R +M SG + P
Sbjct: 687 NPIYMMADSGARG---SASQIR------QLAGMR-GLMAKPSGEIIE--TP--------- 725
Query: 353 FVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLV 396
+ F G+ E+F R+GL DTA+KT+ SGYL R LV
Sbjct: 726 -IKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLV 768
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA
polymerase IV, C-terminal domain. Higher plants have
five multi-subunit nuclear RNA polymerases: RNAP I, RNAP
II and RNAP III, which are essential for viability; plus
the two isoforms of the non-essential polymerase RNAP IV
(IVa and IVb), which specialize in small RNA-mediated
gene silencing pathways. RNAP IVa and/or RNAP IVb might
be involved in RNA-directed DNA methylation of endogenous
repetitive elements, silencing of transgenes, regulation
of flowering-time genes, inducible regulation of adjacent
gene pairs, and spreading of mobile silencing signals.
NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b
is the largest subunit of RNAP IVb. The full subunit
compositions of RNAP IVa and RNAP IVb are not known, nor
are their templates or enzymatic products. However, it
has been shown that RNAP IVa and, to a lesser extent,
RNAP IVb are crucial for several RNA-mediated gene
silencing phenomena.
Length = 381
Score = 56.7 bits (137), Expect = 3e-08
Identities = 38/148 (25%), Positives = 64/148 (43%), Gaps = 6/148 (4%)
Query: 861 EEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 920
EE K + ++ L+D + I + S GI+AA ++ +++
Sbjct: 227 EESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAV 286
Query: 921 AVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLN------PSFIQKMTFEMPLEKIRQ 974
++ G V HL LVAD MT+SG +V +N G + + + F P++ +
Sbjct: 287 SMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLK 346
Query: 975 ASMQGREDSLRAPSARVMLGQECRQGTG 1002
A+ +G DSL G+E GTG
Sbjct: 347 AAKKGASDSLSGVLDACAWGKEAPVGTG 374
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 56.5 bits (137), Expect = 8e-08
Identities = 20/33 (60%), Positives = 25/33 (75%), Gaps = 3/33 (9%)
Query: 567 NLLSLANPGENVGVLAAQSIGEPSTQMTLNTFH 599
+L+ L GE VG++A QSIGEP TQ+TL TFH
Sbjct: 310 DLVEL---GEAVGIIAGQSIGEPGTQLTLRTFH 339
Score = 40.7 bits (96), Expect = 0.004
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 366 EFFFHCMAGREGLIDTAVKTSRSGYLQRCLV 396
E+ C R+G++DTAV+T+ +GYL R LV
Sbjct: 177 EYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 54.4 bits (132), Expect = 9e-08
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 13 KAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISG 46
+AEA LM V + L PK+G P+ G IQD ++
Sbjct: 261 RAEARELMLVPNNILSPKNGKPIIGPIQDMLLGL 294
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 56.0 bits (135), Expect = 9e-08
Identities = 24/46 (52%), Positives = 33/46 (71%)
Query: 573 NPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREI 618
N G VG++AAQSIGEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 972 NIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAEL 1017
Score = 50.6 bits (121), Expect = 4e-06
Identities = 39/133 (29%), Positives = 59/133 (44%), Gaps = 29/133 (21%)
Query: 284 LPEGLIEPFPANN-LQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMM-VSGRTLPSF 341
+ E ++ F +N + M +SGA+G+ Q L G R M + G +
Sbjct: 774 VGEAMLAGFDEDNPIYMMADSGARGNIKQIRQ---------LAGMRGLMADMKGEIID-- 822
Query: 342 LPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEG 401
LP + F G+ E+F R+GL+DTA++T+ SGYL R LV
Sbjct: 823 LP----------IKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVD---- 868
Query: 402 LTVHYDMTVRDSD 414
V D+ VR+ D
Sbjct: 869 --VAQDVIVREED 879
Score = 34.8 bits (80), Expect = 0.31
Identities = 22/100 (22%), Positives = 44/100 (44%), Gaps = 16/100 (16%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVN-QEEDNDFEE 792
+++R++ DD+ D+ E D ERD V+ ED++F +
Sbjct: 143 KEAREEDADDLRDELAADLE-----------ELDAERDRLIEATRRLSVDYVPEDDEFVD 191
Query: 793 P-EDEERMSEREEDDNTSNIGERF---KIEFRDSTNVFVK 828
D+ER++ E ++I E + K R++ + F++
Sbjct: 192 DIGDDERLTAEEVRAEVADIYEEYNERKALRREAFDAFMQ 231
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 56.1 bits (135), Expect = 1e-07
Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 571 LANPGENVGVLAAQSIGEPSTQMTLNTFHFAG 602
++ PGE VGV+AAQSIGEP TQ+TL TFH G
Sbjct: 2273 MSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGG 2304
Score = 43.0 bits (101), Expect = 0.001
Identities = 30/102 (29%), Positives = 47/102 (46%), Gaps = 20/102 (19%)
Query: 295 NNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFV 354
N++ M +SGA+GS Q+S + G L K ++ +P +
Sbjct: 2085 NSIYMMADSGARGSAAQIRQLSAMRG---LMTKPDGSIIE------------TP-----I 2124
Query: 355 DGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLV 396
F G+ E+F R+GL DTA+KT+ +GYL R L+
Sbjct: 2125 ISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLI 2166
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 53.5 bits (129), Expect = 5e-07
Identities = 19/28 (67%), Positives = 23/28 (82%)
Query: 575 GENVGVLAAQSIGEPSTQMTLNTFHFAG 602
GE VG++AAQSIGEP TQ+T+ TFH G
Sbjct: 311 GEAVGIIAAQSIGEPGTQLTMRTFHTGG 338
Score = 40.0 bits (94), Expect = 0.007
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 6/40 (15%)
Query: 375 REGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSD 414
R+GL+DTA++T+ SGYL R LV V D+ VR+ D
Sbjct: 180 RKGLVDTALRTADSGYLTRRLVD------VSQDVIVREED 213
Score = 31.9 bits (73), Expect = 2.1
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 898 YMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 940
Y A+ ++ R ++ EV+NV+ G+++ +H+ ++ MT
Sbjct: 1079 YEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMT 1121
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 50.2 bits (120), Expect = 6e-06
Identities = 20/32 (62%), Positives = 25/32 (78%)
Query: 571 LANPGENVGVLAAQSIGEPSTQMTLNTFHFAG 602
L + GE VG++AAQSIGEP TQ+T+ TFH G
Sbjct: 305 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGG 336
Score = 47.5 bits (113), Expect = 4e-05
Identities = 63/265 (23%), Positives = 101/265 (38%), Gaps = 61/265 (23%)
Query: 153 ILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQER 212
++DKK + L+ + T+G ++ L L Y R G ++ V D+ V
Sbjct: 6 VVDKKALKN----LISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPA- 60
Query: 213 DRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDR---QYK 269
K+ + + + G EI + +F+ ID +
Sbjct: 61 --KQDLLEAAEKEIRATEERYRRG-------EI---------TEVERFQKVIDTWNGTNE 102
Query: 270 SLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRP 329
L D+V NN Q P N++ M SGA+G N Q+ L+G L
Sbjct: 103 ELKDEVVNNFRQTD---------PLNSVYMMAFSGARG---NMSQVRQLVGMRGLMANPQ 150
Query: 330 AMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSG 389
++ LP + + F G+ E+ R+GL+DTA++T+ SG
Sbjct: 151 GEIID-------LPIKTN----------FREGLTVTEYVISSYGARKGLVDTALRTADSG 193
Query: 390 YLQRCLVKHLEGLTVHYDMTVRDSD 414
YL R LV V D+ VR+ D
Sbjct: 194 YLTRRLVD------VSQDVIVREED 212
Score = 36.8 bits (85), Expect = 0.078
Identities = 31/144 (21%), Positives = 57/144 (39%), Gaps = 39/144 (27%)
Query: 898 YMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTH-------------SGT 944
Y A+ ++ R ++ EV+NV+ G+++ +H+ ++ MT G
Sbjct: 1078 YEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGE 1137
Query: 945 YV----------AMNRNG---IRLNP-------------SFIQKMTFEMPLEKIRQASMQ 978
V AM G + P SFI +F+ + +A+++
Sbjct: 1138 LVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIE 1197
Query: 979 GREDSLRAPSARVMLGQECRQGTG 1002
G+ D LR V++G+ GTG
Sbjct: 1198 GKSDWLRGLKENVIIGRLIPAGTG 1221
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 47.3 bits (112), Expect = 4e-05
Identities = 19/28 (67%), Positives = 23/28 (82%)
Query: 575 GENVGVLAAQSIGEPSTQMTLNTFHFAG 602
GE VGV+AAQS+GEP TQ+T+ TFH G
Sbjct: 2333 GEAVGVIAAQSVGEPGTQLTMRTFHIGG 2360
Score = 46.2 bits (109), Expect = 1e-04
Identities = 37/102 (36%), Positives = 46/102 (45%), Gaps = 20/102 (19%)
Query: 295 NNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFV 354
N++ MV SGA+GST Q L G R M T PS E +
Sbjct: 2141 NSVYMMVNSGARGSTSQMKQ---------LAGMRGLM-----TKPSGEIIETP------I 2180
Query: 355 DGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLV 396
F G+ E+F R+GL DTA+KT+ SGYL R LV
Sbjct: 2181 ISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLV 2222
Score = 42.3 bits (99), Expect = 0.002
Identities = 40/178 (22%), Positives = 74/178 (41%), Gaps = 46/178 (25%)
Query: 865 SKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYG 924
SKH++ +G +F+ + L+D + D+H + G+EA +I E++ V+ + G
Sbjct: 2614 SKHVIVNEG---DFVRKGDLLMDGDP----DLHDILRVLGLEALAHYMISEIQQVYRLQG 2666
Query: 925 IEVDPRHLSLV-------------ADYMTHSGTYV----------AMNRNGIR------- 954
+ +D +HL ++ D M G + AM+ +G R
Sbjct: 2667 VRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYLPI 2726
Query: 955 ---------LNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVMLGQECRQGTGL 1003
SFI +F+ + + +A+ G+ D L V++G+ GTGL
Sbjct: 2727 LQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 43.3 bits (102), Expect = 5e-04
Identities = 18/111 (16%), Positives = 41/111 (36%), Gaps = 7/111 (6%)
Query: 704 IIDHFERKFLKELEV--AIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGR 761
+++ K L + K A+ + ++ + D +++E E + + +
Sbjct: 128 VLESIMEGLDKILGIETKAKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESKSEESA 187
Query: 762 VDVS---SDEERDEEDAVQSHKKV--NQEEDNDFEEPEDEERMSEREEDDN 807
D S +E+ D ED Q + + +E+ E P E + +
Sbjct: 188 EDDSDDEEEEDSDSEDYSQYDGMLVDSSDEEEGEEAPSINYNEDTSESESD 238
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 41.5 bits (98), Expect = 0.002
Identities = 24/208 (11%), Positives = 71/208 (34%), Gaps = 8/208 (3%)
Query: 620 MMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEPHM 679
A+ + + E K ++ + I A +K ++ ++
Sbjct: 2 TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61
Query: 680 NYQMKFCFIPAHMY--RDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSR 737
+ + + + KT+ K + ++K EL+ + L +
Sbjct: 62 MVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYV 121
Query: 738 DQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFE--EPED 795
++ + D+ + + +D ++ D+++ + +D D E E ++
Sbjct: 122 KDIDVLNQADDDDDDD----DDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKE 177
Query: 796 EERMSEREEDDNTSNIGERFKIEFRDST 823
E++S+ ++ + E + +D+
Sbjct: 178 LEKLSDDDDFVWDEDDSEALRQARKDAK 205
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 38.9 bits (91), Expect = 0.004
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEP 793
E D E+D E E + + SSDEE + + ++ + EE+ F
Sbjct: 4 ESESDDGEEDEELPEEDEDDE----------SSDEEEVDLPDDEQDEESDSEEEQIFVTR 53
Query: 794 EDEERMSEREED 805
++EE E E +
Sbjct: 54 QEEEVDPEAEAE 65
Score = 28.9 bits (65), Expect = 8.2
Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEP 793
++ + ++D E + E + + S+EE+ + ++V+ E + +F+
Sbjct: 13 DEELPEEDEDDESSDEEEVDL-PDDEQDEESDSEEEQIFVT--RQEEEVDPEAEAEFDR- 68
Query: 794 EDEERMSE 801
E E+ M+E
Sbjct: 69 EFEKMMAE 76
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 39.3 bits (92), Expect = 0.008
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 18/107 (16%)
Query: 720 IAKRAAQGLKNMNIEQSRDQMEDD-------VEDDEGEGAEGAGAALGRVDVSSDEER-- 770
+ K + K EQ + +DD VE+DE EG +DV SD+E
Sbjct: 75 LEKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEG-----EWIDVESDKEIES 129
Query: 771 ----DEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGE 813
DEE+ ++ KK ++ D + E ++EE E E + E
Sbjct: 130 SDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEKASE 176
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 39.2 bits (91), Expect = 0.015
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 13/64 (20%)
Query: 741 EDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMS 800
+ + + DE +G +G G + G S+EE +EE+ +EE+ + EE E+EE
Sbjct: 842 QGEAKQDE-KGVDGGGGSDGG---DSEEEEEEEE---------EEEEEEEEEEEEEEEEE 888
Query: 801 EREE 804
E EE
Sbjct: 889 ENEE 892
Score = 32.3 bits (73), Expect = 1.8
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 14/84 (16%)
Query: 741 EDDVEDDEGEGAEGAGAALGRVDVSSDEER----DEEDAVQSHKKVN----------QEE 786
+ E DE EG A V + E+ ++ +A Q K V+ +EE
Sbjct: 807 TEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEE 866
Query: 787 DNDFEEPEDEERMSEREEDDNTSN 810
+ + EE E+EE E EE++ N
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEEN 890
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 38.8 bits (91), Expect = 0.016
Identities = 32/129 (24%), Positives = 56/129 (43%), Gaps = 20/129 (15%)
Query: 709 ERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVE---DDEGEGAE-------GAGAA 758
E + LK+LE A+R L+ M E+ D+ E+D + DD + E G G
Sbjct: 267 EAERLKKLE---AER----LRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQG 319
Query: 759 LGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSN---IGERF 815
+ D DE++ +EED D + E++E + +++D+ E+
Sbjct: 320 EEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKK 379
Query: 816 KIEFRDSTN 824
K + +ST
Sbjct: 380 KKKSAESTR 388
Score = 31.5 bits (72), Expect = 3.1
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 731 MNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHK 780
I++ D +DD DD+ G + D+E DEE+ + K
Sbjct: 124 SEIDKDDDVRDDDDFDDDDLGDLASDDRAAHFGGGEDDEEDEEEQPERKK 173
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 36.5 bits (84), Expect = 0.057
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 748 EGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEED--NDFEEPEDEERMSEREED 805
+ +G G ++SS++ D + ++ + E ND++E ED + + D
Sbjct: 242 RSDDDQGYGRYKQ--NLSSNKYGDFKGVNYGYESDDDEGSSSNDYDEEEDGDDDDNEDND 299
Query: 806 DNTSNIGER 814
D +N G+
Sbjct: 300 DTNTNHGDE 308
Score = 30.7 bits (69), Expect = 3.7
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 11/77 (14%)
Query: 737 RDQMEDDVEDDEGEGA--------EGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDN 788
R +DD+G G + SD++ + ++ D+
Sbjct: 236 RQTRGFRSDDDQGYGRYKQNLSSNKYGDFKGVNYGYESDDDEGSSS---NDYDEEEDGDD 292
Query: 789 DFEEPEDEERMSEREED 805
D E D+ + +ED
Sbjct: 293 DDNEDNDDTNTNHGDED 309
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 36.5 bits (84), Expect = 0.060
Identities = 21/93 (22%), Positives = 35/93 (37%), Gaps = 8/93 (8%)
Query: 730 NMNIEQSRDQMEDDVED-----DEGEGAEGAGAALGRVDVSS---DEERDEEDAVQSHKK 781
N + DVE+ DE + A RV + D + D ++A +
Sbjct: 114 NNEYPGITKLEKSDVEEPSEKVDEEDVEREILAEKPRVTRFNIVWDNDEDNDEAPPAQPD 173
Query: 782 VNQEEDNDFEEPEDEERMSEREEDDNTSNIGER 814
V+ EE+ EE + E + E ++ G R
Sbjct: 174 VDNEEEERLEESDGREEEEDEEVGSDSYGEGNR 206
Score = 33.0 bits (75), Expect = 0.63
Identities = 27/131 (20%), Positives = 46/131 (35%), Gaps = 24/131 (18%)
Query: 694 RDKTSVKPSKI-IDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDD----VEDDE 748
+ K+ + ER+ L E + NI D+ D+ D +
Sbjct: 125 KSDVEEPSEKVDEEDVEREILAE---------KPRVTRFNIVWDNDEDNDEAPPAQPDVD 175
Query: 749 GEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED-----EERMSERE 803
E E + GR +EE DEE S+ + N+E + + EE + E+ +
Sbjct: 176 NEEEERLEESDGR-----EEEEDEEVGSDSYGEGNRELNEEEEEEAEGSDDGEDVVDYEG 230
Query: 804 EDDNTSNIGER 814
E + E
Sbjct: 231 ERIDKKQGEEE 241
Score = 31.5 bits (71), Expect = 2.0
Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 10/90 (11%)
Query: 732 NIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQE------ 785
N E+ R + D E++E E E + G + +EE +EE + +
Sbjct: 176 NEEEERLEESDGREEEEDE--EVGSDSYGEGNRELNEEEEEEAEGSDDGEDVVDYEGERI 233
Query: 786 EDNDFEEPEDEERMS--EREEDDNTSNIGE 813
+ EE E EE + E + S E
Sbjct: 234 DKKQGEEEEMEEEVINLFEIEWEEESPSEE 263
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 35.5 bits (82), Expect = 0.082
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 10/76 (13%)
Query: 736 SRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED 795
+ + + E+D E L ++ E+ DEED EE+ + EE ED
Sbjct: 137 RKVGLFTEEEEDIDEKLSMLEKKLKELE---AEDVDEEDE-------KDEEEEEEEEEED 186
Query: 796 EERMSEREEDDNTSNI 811
E+ + ++DD+ N
Sbjct: 187 EDFDDDDDDDDDDYNA 202
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 36.6 bits (84), Expect = 0.088
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 735 QSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPE 794
+SR +EDD +D E + AE + D + D+EDA + + +E+
Sbjct: 696 KSRPDVEDDSDDSELDFAEDDFSDSTSDDEPKLDAIDDEDAKSEGSQESDQEEG-----L 750
Query: 795 DEERMSEREEDDNTSNIGE 813
DE S E DN+ + E
Sbjct: 751 DEIFYSFDGEQDNSDSFAE 769
Score = 30.0 bits (67), Expect = 8.4
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 15/92 (16%)
Query: 731 MNIEQSRDQMEDDVEDDE--------GEGAEGAGAALGRVDVSSDEERDEEDA----VQS 778
+N E + +D++ ++ + A+G G + SD+E DE + V+S
Sbjct: 638 VNTEDWLTKKVEDIKPEDKFFYQYFTKKTADGKGKKSNKASFDSDDEMDENEIWSALVKS 697
Query: 779 HKKV-NQEEDNDFEEPEDEERMSEREEDDNTS 809
V + +D++ + ED+ S+ DD
Sbjct: 698 RPDVEDDSDDSELDFAEDD--FSDSTSDDEPK 727
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 35.1 bits (81), Expect = 0.13
Identities = 26/125 (20%), Positives = 43/125 (34%), Gaps = 16/125 (12%)
Query: 688 IPAHM---YRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIE-----QSRDQ 739
+PAH YR ++ R ELE A ++ + IE + D
Sbjct: 35 LPAHTKLKYRQPGQGTEDELRK---RDLRAELEEAERAHKSKKENKLAIEDADKSTNLDA 91
Query: 740 MEDDVEDDEGEGAEGAGAAL-GRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEER 798
+ EDD+ E + +D+ D+ S + + D+D E E
Sbjct: 92 SNEGDEDDDEEDEIKRKRIEEDARNSDADDSDSSSDSDSS----DDDSDDDDSEDETAAL 147
Query: 799 MSERE 803
+ E E
Sbjct: 148 LRELE 152
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 35.2 bits (81), Expect = 0.14
Identities = 16/80 (20%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 729 KNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDN 788
KN ++E+ ++ D + +G +G+ +++ D+E+ +E++
Sbjct: 214 KNKSLEEYYEKESSDAAASQDDGPKGSDVK--------NKKSDDEEDDDQDGDYVEEKEL 265
Query: 789 DFEEPEDEERMSEREEDDNT 808
+E E+E E EED++
Sbjct: 266 KEDEEEEETEEEEEEEDEDE 285
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 35.2 bits (81), Expect = 0.19
Identities = 23/106 (21%), Positives = 44/106 (41%), Gaps = 8/106 (7%)
Query: 720 IAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDV--SSDEERDEEDAVQ 777
I +A + L + E Q V D G+ G + +DEE ++D
Sbjct: 184 IEDKAGEDLDGLAAEIDDQQAFARVVRDML-GSMDMAEETGDDGIEEDADEEDGDDDQPD 242
Query: 778 SHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDST 823
+ N++ + EE E + SE +E + T GE +++ +++
Sbjct: 243 N----NEDSEAGREESEGSDE-SEEDEAEATDGEGEEGEMDAAEAS 283
Score = 34.4 bits (79), Expect = 0.32
Identities = 22/98 (22%), Positives = 35/98 (35%), Gaps = 12/98 (12%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSS----DEERDEEDAVQSHKKVNQEEDND 789
E D D+ ED E E G+ D + + E E DA ++ E+
Sbjct: 234 EDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEA-----SEDSES 288
Query: 790 FEEPEDEERMSEREEDDNTS-NIGERFKIEFRDSTNVF 826
E ED E E + E +++++ T F
Sbjct: 289 DESDEDTETPGEDARPATPFTELME--EVDYKVFTREF 324
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 33.0 bits (75), Expect = 0.22
Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 11/93 (11%)
Query: 714 KELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEE 773
++LE A RA +G + + E+ D E A+ A A D + +
Sbjct: 48 RDLEWTEAGRAEKGPAAAATAAA-EAAEEAEAADADEDADEAAEA--------DAADEAD 98
Query: 774 DAVQSHKKVNQEEDNDFEEPE--DEERMSEREE 804
+ ++ + V++ D E E DEE E E
Sbjct: 99 EEEETDEAVDETADEADAEAEEADEEEDEEAEA 131
Score = 31.1 bits (70), Expect = 1.3
Identities = 13/69 (18%), Positives = 24/69 (34%)
Query: 738 DQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEE 797
+ E AE A A + + + DE D + + E ++ + +E
Sbjct: 62 PAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEA 121
Query: 798 RMSEREEDD 806
E EE +
Sbjct: 122 DEEEDEEAE 130
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 34.5 bits (79), Expect = 0.30
Identities = 16/65 (24%), Positives = 27/65 (41%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEP 793
+Q + +++ + EGEG EG+ E +EE + E D+D E P
Sbjct: 218 DQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESDDDSETP 277
Query: 794 EDEER 798
+ R
Sbjct: 278 GEGAR 282
Score = 31.5 bits (71), Expect = 2.5
Identities = 26/116 (22%), Positives = 49/116 (42%), Gaps = 11/116 (9%)
Query: 692 MYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVED-DEGE 750
++R+ K K +D + + A A+ + L++M + + +M DD E DE +
Sbjct: 160 LWRNDIEAKAGKDLDRLSAAI--DDQQAFARVVREMLRSMELAE---EMGDDTESEDEED 214
Query: 751 GAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDD 806
G + + +E+ + E Q + E D E EE M + ++DD
Sbjct: 215 GDDDQPT-----ENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDD 265
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 34.5 bits (79), Expect = 0.31
Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEP 793
E+ + E++ E++E E + + + E+ +EE+ V++ +E + E
Sbjct: 441 EEESVEEEEEEEEEEEEEEQES-------EEEEGEDEEEEEEVEADNGSEEEMEGSSEGD 493
Query: 794 EDEERMSEREEDDNTSNIG 812
D E E E N+ G
Sbjct: 494 GDGEEPEEDAERRNSEMAG 512
Score = 32.6 bits (74), Expect = 1.3
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 767 DEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGE 813
+EE +EE+ + ++ +EE D EE E+ E + EE+ S+ G+
Sbjct: 447 EEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGD 493
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 33.6 bits (77), Expect = 0.56
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 3/65 (4%)
Query: 741 EDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMS 800
D+ ED+E E + S +E + S + + + +D E D+E S
Sbjct: 370 VDEDEDEEEEQRSDEH-EEEEGEDSEEEGSQSREDGSS--ESSSDVGSDSESKADKESAS 426
Query: 801 EREED 805
+ + +
Sbjct: 427 DSDSE 431
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 33.6 bits (78), Expect = 0.61
Identities = 29/121 (23%), Positives = 44/121 (36%), Gaps = 34/121 (28%)
Query: 714 KELEVAIAKRAAQGLKNMNIEQSRDQME-----------------DDVEDDEGEGAEGAG 756
+E E+ IAKR IE + M D +E+ E E
Sbjct: 121 REGEIEIAKR---------IEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRE--- 168
Query: 757 AALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMS-EREEDDNTSNIGERF 815
+D D +E+ A + ++D D EE EDE S +E + + E+F
Sbjct: 169 ----LIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKF 224
Query: 816 K 816
K
Sbjct: 225 K 225
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 33.0 bits (76), Expect = 0.62
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 29/111 (26%)
Query: 233 NALGLPLDTDPEIISSQLQE--AYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIE 290
+G + DPE++ + IP ++ K+T NI +
Sbjct: 143 RGMGAAVGQDPELVEEICRWVREAVKIP------------VIAKLTPNITDIR------- 183
Query: 291 PFPANNLQFMVESGAKG-STVNTMQISCLLGQIELEGKRPAMMVSGRTLPS 340
A + E GA G S +NT ++ L+G ++L+G PA V G+T
Sbjct: 184 -EIARAAK---EGGADGVSAINT--VNSLMG-VDLDGTPPAPGVEGKTTYG 227
>gnl|CDD|151958 pfam11521, TFIIE-A_C-term, C-terminal general transcription factor
TFIIE alpha. TFIIE is compiled of two subunits, alpha
and beta. This family of proteins are the C terminal
domain of the alpha subunit of the protein which is the
largest subunit and contains several functional domains
which are important for basal transcription and cell
growth. The C terminal end of the protein binds directly
to the amino-terminal PH domain of p62/Tfb1 (of IIH)
which is involved in the recruitment of the general
transcription factor IIH to the transcription
preinitiation complex. P53 competes for the same binding
site as TFIIE alpha which shows their structural
similarity. Like p53, TFIIE alpha 336-439 can activate
transcription in vivo.
Length = 86
Score = 30.9 bits (70), Expect = 0.63
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 765 SSDEERDEED-------AVQSHKKVNQEEDNDFEEPEDE 796
SD ++D A QS + +ED++FEE EDE
Sbjct: 2 ESDTSESDDDSPSPEPPAGQSVDEEEDDEDDEFEEVEDE 40
>gnl|CDD|222405 pfam13830, DUF4192, Domain of unknown function (DUF4192).
Length = 321
Score = 33.1 bits (76), Expect = 0.64
Identities = 15/58 (25%), Positives = 17/58 (29%), Gaps = 3/58 (5%)
Query: 718 VAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDA 775
VA A G SR +E G AE AAL + D A
Sbjct: 138 VAAAAAVLAG---RVPLLSRADLEARFAPPPGAAAERLAAALDAAARARDARLARLPA 192
>gnl|CDD|217830 pfam03986, Autophagy_N, Autophagocytosis associated protein (Atg3),
N-terminal domain. Autophagocytosis is a
starvation-induced process responsible for transport of
cytoplasmic proteins to the lysosome/vacuole. Atg3 is a
ubiquitin like modifier that is topologically similar to
the canonical E2 enzyme. It catalyzes the conjugation of
Atg8 and phosphatidylethanolamine.
Length = 146
Score = 31.9 bits (73), Expect = 0.64
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 12/99 (12%)
Query: 701 PSKIIDHF--ERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAA 758
PSKI + +++FL V +RA Q D E+ VED++ + G
Sbjct: 54 PSKIRPYLPPDKQFLVTRNVPCYRRAKQMEYG-------DGAEEIVEDEDEDD--GWVTT 104
Query: 759 LGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEE 797
G D ++ +E+ + + + + + ED++
Sbjct: 105 HGNRD-KQKDDIADEEDIPEIGDDDDDVVDSSDADEDDD 142
>gnl|CDD|147374 pfam05160, DSS1_SEM1, DSS1/SEM1 family. This family contains the
breast cancer tumour suppressor BRCA2-interacting
protein DSS1 and its homologue SEM1, both of which are
short acidic proteins. DSS1 has been shown to be a
conserved component of the Rae1 mediated mRNA export
pathway in Schizosaccharomyces pombe.
Length = 63
Score = 30.0 bits (68), Expect = 0.69
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 774 DAVQSHKKVNQEEDNDFEE-PEDEERMSEREEDD 806
+ KK EED++FE+ P ++ E E+++
Sbjct: 1 QKKEQVKKKLLEEDDEFEDFPVEDWPEEETEKEN 34
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 33.1 bits (76), Expect = 0.84
Identities = 27/118 (22%), Positives = 43/118 (36%), Gaps = 16/118 (13%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGA-----GAALGRVDVSSDEERDE--------EDAVQSHK 780
E E++ EDD+ + +G LG++ D+E + + A K
Sbjct: 328 EDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDDEENSGLLSMKFMQRAEARKK 387
Query: 781 KVNQEEDNDF-EEPEDEERMSEREEDDN-TSNIGER-FKIEFRDSTNVFVKDVVNQHN 835
+ N E + E E EE E E ++ N+G R F E + K N
Sbjct: 388 EENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKN 445
Score = 31.2 bits (71), Expect = 3.4
Identities = 25/123 (20%), Positives = 51/123 (41%), Gaps = 10/123 (8%)
Query: 708 FERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGR----VD 763
KF++ E A++ + IE+ R ++E + E DE E E + +GR +
Sbjct: 374 LSMKFMQRAE---ARKKEENDAE--IEELRRELEGEEESDEEENEEPSKKNVGRRKFGPE 428
Query: 764 VSSDEERDEEDAVQSHKKVNQE-EDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDS 822
E ++ ++ + ++ E ++ EE EDEE + + E+ + E +
Sbjct: 429 NGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEE 488
Query: 823 TNV 825
Sbjct: 489 ELD 491
>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D. SpoVID, the
stage VI sporulation protein D, is restricted to
endospore-forming members of the bacteria, all of which
are found among the Firmicutes. It is widely distributed
but not quite universal in this group. Between
well-conserved N-terminal and C-terminal domains is a
poorly conserved, low-complexity region of variable
length, rich enough in glutamic acid to cause spurious
BLAST search results unless a filter is used. The seed
alignment for this model was trimmed, in effect, by
choosing member sequences in which these regions are
relatively short. SpoVID is involved in spore coat
assembly by the mother cell compartment late in the
process of sporulation [Cellular processes, Sporulation
and germination].
Length = 338
Score = 32.9 bits (75), Expect = 0.86
Identities = 22/111 (19%), Positives = 36/111 (32%), Gaps = 14/111 (12%)
Query: 709 ERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEG-AGAALGRVDVSSD 767
E F E E + A + + E VE + E E A +S+
Sbjct: 154 EESFSAEFEHPAQEETAGEEERTD--------EPKVEHEAHEQHEQPADDDPDEWKISAS 205
Query: 768 EERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIE 818
E + E+ ++EE EDE + +E+ E + E
Sbjct: 206 EP-----FQLESEVEASPEEENYEEYEDETELEVEDEEKALDEQTEDPQQE 251
Score = 30.2 bits (68), Expect = 5.3
Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 12/100 (12%)
Query: 738 DQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEE----------D 787
+ +D E++E AE A + + + +EER +E V+ E+
Sbjct: 145 EPAREDEEEEESFSAEFEHPA--QEETAGEEERTDEPKVEHEAHEQHEQPADDDPDEWKI 202
Query: 788 NDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFV 827
+ E + E + E++N + ++E D
Sbjct: 203 SASEPFQLESEVEASPEEENYEEYEDETELEVEDEEKALD 242
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The CAF-1
or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression in
addition to DNA-based checkpoints.
Length = 76
Score = 30.3 bits (69), Expect = 0.90
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 763 DVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDD 806
D SD E +EE+ ED + E+ EDEE + + D
Sbjct: 41 DYDSDAEWEEEEE---------GEDLESEDEEDEEEDDDDDMDG 75
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 33.4 bits (76), Expect = 0.91
Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 6/96 (6%)
Query: 715 ELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEED 774
++E A + + Q D +E++ DE + D++ D+E+ ED
Sbjct: 4012 DMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDF------SDLAEDDEKMNED 4065
Query: 775 AVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSN 810
+ + + N+E D + ++E E ED N
Sbjct: 4066 GFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDN 4101
Score = 32.7 bits (74), Expect = 1.5
Identities = 30/143 (20%), Positives = 52/143 (36%), Gaps = 27/143 (18%)
Query: 736 SRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDE---EDAVQSHKKVNQEEDNDFEE 792
S D ++ E E G G+ +G D+++ D+ E A EED +
Sbjct: 3799 SPDLPQEKSNSGELESGTGLGSGVGAEDITNTLNEDDDLEELA--------NEEDTANQS 3850
Query: 793 PEDEERMSEREEDDN---TSNIGERFKIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMW 849
DE E E D N ++ + + N + + VN S ++K +W
Sbjct: 3851 DLDESEARELESDMNGVTKDSVVSENENSDSEEENQDLDEEVNDIPEDLSNSLNEK--LW 3908
Query: 850 CKLLFLPSNLFEEKESKHLLKTD 872
+E + LL+T+
Sbjct: 3909 -----------DEPNEEDLLETE 3920
Score = 32.3 bits (73), Expect = 2.0
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 8/84 (9%)
Query: 729 KNMNIEQSRDQMEDDV------EDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKV 782
K+ ++ ++M DDV + D E +D+ D + DE++ K
Sbjct: 3948 KDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEG-DVSKDS 4006
Query: 783 NQEEDNDFEEPEDEERMSEREEDD 806
+ ED D E ++ + ++ E+D+
Sbjct: 4007 DL-EDMDMEAADENKEEADAEKDE 4029
Score = 31.9 bits (72), Expect = 2.5
Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 17/103 (16%)
Query: 714 KELEVAIAKRAAQGLKNMN--IEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERD 771
ELE + G +++ + + D E E+D + D+ E R+
Sbjct: 3810 GELESGTGLGSGVGAEDITNTLNEDDDLEELANEEDTAN----------QSDLDESEARE 3859
Query: 772 EEDAV-----QSHKKVNQEEDNDFEEPEDEERMSEREEDDNTS 809
E + S N+ D++ E + +E +++ ED + S
Sbjct: 3860 LESDMNGVTKDSVVSENENSDSEEENQDLDEEVNDIPEDLSNS 3902
Score = 31.5 bits (71), Expect = 2.8
Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 11/91 (12%)
Query: 734 EQSRDQMEDDVEDDEGEGA------EGAGAALGRVDVSSDE---ERDEEDAVQSHKKVNQ 784
Q D+ +D+ +D E L + S+E +E D V
Sbjct: 3885 NQDLDEEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKA 3944
Query: 785 EEDNDFEEPEDEERMSER--EEDDNTSNIGE 813
ED D +E EDEE MS+ +D+ +I E
Sbjct: 3945 LEDKDRQEKEDEEEMSDDVGIDDEIQPDIQE 3975
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 33.1 bits (75), Expect = 0.97
Identities = 20/99 (20%), Positives = 44/99 (44%), Gaps = 13/99 (13%)
Query: 710 RKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEE 769
+ + +L++ I KR +++ E + ++DD+ + D D+E
Sbjct: 121 KAEIGDLDMIIIKRRRA--RHLAEEDMSPRDNFVIDDDDEDE-----------DEDDDDE 167
Query: 770 RDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNT 808
D+E+ + +++ +D D E+ E+ E+ E D T
Sbjct: 168 EDDEEEEEEEEEIKGFDDEDEEDEGGEDFTYEKSEVDKT 206
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 32.6 bits (74), Expect = 1.2
Identities = 26/127 (20%), Positives = 51/127 (40%), Gaps = 6/127 (4%)
Query: 709 ERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDE 768
E+ K+ ++A K+ K D E D +D + EG E + + E
Sbjct: 239 EKSKKKKKKLAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSASGNDPE 298
Query: 769 ER-----DEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDST 823
ER E A ++ E+++ E+ E+E +S++ + G++ ++ DS
Sbjct: 299 EREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKK-LKGKKNGLDKDDSD 357
Query: 824 NVFVKDV 830
+ D
Sbjct: 358 SGDDSDD 364
Score = 29.9 bits (67), Expect = 8.2
Identities = 24/123 (19%), Positives = 46/123 (37%), Gaps = 29/123 (23%)
Query: 703 KIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRV 762
K + F+ +K A G D+ E+ EGE G ++
Sbjct: 173 KTANGFQLMMMK--------AAKNG---------PAAFGDEDEETEGEKGGGGRGKDLKI 215
Query: 763 -DVSSDEE---------RDEEDAVQSHKKVNQEEDNDFEEPEDEE--RMSEREEDDNTSN 810
D+ D+E ++ D +S KK + N + +D++ R + + D+ S+
Sbjct: 216 KDLEGDDEDDGDESDKGGEDGDEEKSKKKKKKLAKNKKKLDDDKKGKRGGDDDADEYDSD 275
Query: 811 IGE 813
G+
Sbjct: 276 DGD 278
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM). This
family consists of several Plasmodium falciparum SPAM
(secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the alanine
heptad-repeat domain. Heptad repeats in which the a and
d position contain hydrophobic residues generate
amphipathic alpha-helices which give rise to helical
bundles or coiled-coil structures in proteins. SPAM is
an example of a P. falciparum antigen in which a
repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 31.4 bits (71), Expect = 1.3
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 771 DEEDAVQSHKKVNQE--EDNDFEEPEDEERMSEREEDDNTSNIGE 813
D+ED ++ ++ V E ED++ EE EDEE + E E+ ++ I E
Sbjct: 32 DKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVE 76
Score = 30.2 bits (68), Expect = 3.7
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 768 EERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFV 827
+E DEE+ + +++ + ED + EE E+ E E++++ ++ + K D N
Sbjct: 48 QEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNS-T 106
Query: 828 KDVVNQHNIVHKYSYDKKN 846
+D Q+ I Y ++K+
Sbjct: 107 QDDNAQNLISKNYKKNEKS 125
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 32.5 bits (74), Expect = 1.5
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 17/85 (20%)
Query: 731 MNIEQSRDQMEDD-----VEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQE 785
+N +S D +DD EDDE + + +S E ++D++ +++
Sbjct: 80 LNQRKSLDDDDDDEFDFLYEDDEDDAG----------NATSGESSTDDDSLLE--LPDRD 127
Query: 786 EDNDFEEPEDEERMSEREEDDNTSN 810
ED D + D+ ++++ N+
Sbjct: 128 EDADTQANNDQTNDFDQDDSSNSQT 152
>gnl|CDD|234932 PRK01269, PRK01269, tRNA s(4)U8 sulfurtransferase; Provisional.
Length = 482
Score = 32.1 bits (74), Expect = 1.8
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 694 RDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAE 753
+ KI + E+KF + AI R + +N++I + +Q E +V + E
Sbjct: 350 KPTVKAVKEKI-EAEEKKF----DFAILDRVVEEARNIDIREIAEQTEQEVVEVETVSEL 404
Query: 754 GAGAALGRVDVSSDEERDE 772
+ +D+ S +E+++
Sbjct: 405 PPDDVI--IDIRSPDEQED 421
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 32.1 bits (72), Expect = 2.1
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 738 DQMEDDVEDDEGEGAEGAGAALGRVDVSSDE---ERDEEDAVQSHKKVNQEEDNDFEEPE 794
D M DD+E D+ E A D ++++ ERD+ DAV+ ++ D+ +
Sbjct: 405 DTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSMADDTAIDSM 464
Query: 795 DEERMSER--EEDDN 807
++ S+ E DD
Sbjct: 465 ADDAASDAVAESDDG 479
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 31.9 bits (73), Expect = 2.2
Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 760 GRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEF 819
G ++ +E +DA + + +++D+D E E++E S+ E+D++ + + I
Sbjct: 104 GDIEEELQDEPRYDDAYR---DLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIAT 160
Query: 820 R 820
R
Sbjct: 161 R 161
Score = 31.1 bits (71), Expect = 4.0
Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 8/75 (10%)
Query: 738 DQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDE- 796
D + + E + + A L D +E +E++ + ++D+D ++
Sbjct: 102 DDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATR 161
Query: 797 -------ERMSEREE 804
R E EE
Sbjct: 162 ERSLERRRRRREWEE 176
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 31.2 bits (71), Expect = 2.3
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 10/65 (15%)
Query: 741 EDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMS 800
E+++E+DE EE D+E+ ++ +E D+DF++ ED+E S
Sbjct: 19 EEELEEDEFFWTYLLFE----------EEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPES 68
Query: 801 EREED 805
+ EE+
Sbjct: 69 DDEEE 73
>gnl|CDD|237056 PRK12321, cobN, cobaltochelatase subunit CobN; Reviewed.
Length = 1100
Score = 31.9 bits (73), Expect = 2.3
Identities = 20/56 (35%), Positives = 23/56 (41%), Gaps = 10/56 (17%)
Query: 205 DILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQF 260
D L + RDR I ++AR G EA GL DT P EA I F
Sbjct: 617 DGLDPRRRDRLARAIRDEARAAGLEADA---GLDADTPPA-------EALTRIDAF 662
>gnl|CDD|238450 cd00885, cinA, Competence-damaged protein. CinA is the first gene
in the competence- inducible (cin) operon and is thought
to be specifically required at some stage in the process
of transformation. This domain is closely related to a
domain, found in a variety of proteins involved in
biosynthesis of molybdopterin cofactor, where the domain
is presumed to bind molybdopterin.
Length = 170
Score = 30.5 bits (70), Expect = 2.4
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 16/60 (26%)
Query: 229 EAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLDKVT-NNINQVCLPEG 287
EA A G PL D E +I+ ++ ++T N+ Q LPEG
Sbjct: 78 EAVAKAFGRPLVLDEE---------------ALERIEARFARRGREMTEANLKQAMLPEG 122
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 31.2 bits (70), Expect = 2.6
Identities = 26/119 (21%), Positives = 53/119 (44%), Gaps = 21/119 (17%)
Query: 712 FLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERD 771
++ EV+ + Q + N E +++++ D D+ GE EE D
Sbjct: 283 EIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGE---------------EKEEDD 327
Query: 772 EEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTNVFVKDV 830
E + + H ++ +E N+ E+ +E+R R+ + T+ I + F NV +K++
Sbjct: 328 ENEENERHTELLADELNELEKGIEEKR---RQMESATNPI---LQKRFESQLNVLLKEL 380
Score = 30.1 bits (67), Expect = 6.2
Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 726 QGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQE 785
+ L +++ + E++ E+ E GAA S+ +++++ + + ++E
Sbjct: 250 EPLSRPALKKEKQGAEEEGEEGMSEEDLDVGAAEIENKEVSEGDKEQQQEEVENAEAHKE 309
Query: 786 EDNDFEEPEDEERMSEREEDDNTSNIGERFKIEFRDSTN 824
E E E E+EEDD ER D N
Sbjct: 310 EVQSDRPDEIGE---EKEEDDENEEN-ERHTELLADELN 344
>gnl|CDD|191331 pfam05645, RNA_pol_Rpc82, RNA polymerase III subunit RPC82. This
family consists of several DNA-directed RNA polymerase
III polypeptides which are related to the Saccharomyces
cerevisiae RPC82 protein. RNA polymerase C (III)
promotes the transcription of tRNA and 5S RNA genes. In
Saccharomyces cerevisiae, the enzyme is composed of 15
subunits, ranging from 160 to about 10 kDa.
Length = 215
Score = 30.8 bits (70), Expect = 2.6
Identities = 25/143 (17%), Positives = 42/143 (29%), Gaps = 26/143 (18%)
Query: 769 ERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIG---------------- 812
+ + ++ K E + E PE + R D+T N
Sbjct: 44 TSEIKRRAEAKVKAKTELRDLRESPEILLKGLGRSLADDTDNPTGKKRTKILDPGLVWRV 103
Query: 813 --ERFKIEFRDSTNV-FVKDVVNQ--HNIVH---KYSYDKKNHMWCKLLFLPSNLFEEKE 864
ERF RD V K + + + S + L PS F +
Sbjct: 104 NLERFHKHLRDEALVDLAKSRIGSTTAEVYRAALRLSESRTPPCSAPLSEDPSITFTAND 163
Query: 865 SKHLLKTDGINV-NFISQYRHLL 886
L +++ + Q+ LL
Sbjct: 164 IARALPKS-LDLSMLLDQHLKLL 185
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 30.8 bits (69), Expect = 2.8
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 11/92 (11%)
Query: 720 IAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSH 779
I K+ + ++ IE++R + E+ E E E R + DE D+E+ +
Sbjct: 115 IKKKKSLIIRQEQIEKARQEREELEERMEWE----------RREEKIDEREDQEEQERER 164
Query: 780 KKVNQEEDNDFEEPED-EERMSEREEDDNTSN 810
++ EE +D E E E+ SE E DD+ +
Sbjct: 165 EEQTIEEQSDDSEHEIIEQDESETESDDDKTE 196
Score = 30.4 bits (68), Expect = 3.3
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 2/81 (2%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEP 793
+Q R +DD++ + R + EER E + + +K+++ ED + +E
Sbjct: 105 DQLRSVKKDDIKKKKSLIIRQEQIEKARQEREELEERMEWE--RREEKIDEREDQEEQER 162
Query: 794 EDEERMSEREEDDNTSNIGER 814
E EE+ E + DD+ I E+
Sbjct: 163 EREEQTIEEQSDDSEHEIIEQ 183
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 31.5 bits (71), Expect = 2.9
Identities = 29/150 (19%), Positives = 59/150 (39%), Gaps = 10/150 (6%)
Query: 731 MNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDF 790
M+ E S D E++ ED+ E + D+ ++ E ED + ++E+ +
Sbjct: 109 MDSEDSADDEEEEEEDESLE--DEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEE 166
Query: 791 EEPEDEERMS---EREEDDNTSNIGER-FKIE----FRDSTNVFVKDVVNQHNIVHKYSY 842
EE +E+ RE+ + S + ++ FK++ F ++T + + + Y
Sbjct: 167 EEAGEEKESVEQATREKKFDKSGVDDKFFKLDEMNEFLEATEAEEEAALGDEDDFEDYFQ 226
Query: 843 DKKNHMWCKLLFLPSNLFEEKESKHLLKTD 872
D F E+ E ++ D
Sbjct: 227 DDSEDGKDDEDFGSGEDEEDDEEGNIEYED 256
Score = 30.3 bits (68), Expect = 5.6
Identities = 26/144 (18%), Positives = 52/144 (36%), Gaps = 27/144 (18%)
Query: 705 IDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDE--GEGAEGAGAALGRV 762
+D FL+ E + AA G ++ + +D +D +DDE G G + G +
Sbjct: 197 LDEMNE-FLEATEAE--EEAALGDEDDFEDYFQD-DSEDGKDDEDFGSGEDEEDDEEGNI 252
Query: 763 ---------------DVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDN 807
D D E ++++ + K + + E+ ED+ E++D+
Sbjct: 253 EYEDFFDPKEKDKKKDAGDDAELEDDEPDKEAVKKEADSKPEEEDEEDD------EQEDD 306
Query: 808 TSNIGERFKIEFRDSTNVFVKDVV 831
+ + V + V
Sbjct: 307 QDEEEPPEAAMDKVKLDEPVLEGV 330
Score = 30.0 bits (67), Expect = 7.8
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 4/77 (5%)
Query: 737 RDQMEDDVEDDEGEGAEGAGAALGR----VDVSSDEERDEEDAVQSHKKVNQEEDNDFEE 792
+D+ +D +D E E E A+ + DEE DE++ Q ++ + + +
Sbjct: 263 KDKKKDAGDDAELEDDEPDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKL 322
Query: 793 PEDEERMSEREEDDNTS 809
E + E S
Sbjct: 323 DEPVLEGVDLESPKELS 339
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 31.3 bits (71), Expect = 3.1
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 449 WICSYKVILNLLKKHPLSLALLLLLTFK--------SSGKPNFIFSP 487
W Y V+ +L AL+ +L K SG +F+P
Sbjct: 296 WGNGYSVVNTILHAPWTWQALVAVLVAKLIATAATAGSGAVGGVFTP 342
>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family.
Prothymosin alpha and parathymosin are two ubiquitous
small acidic nuclear proteins that are thought to be
involved in cell cycle progression, proliferation, and
cell differentiation.
Length = 106
Score = 29.2 bits (65), Expect = 3.5
Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 9/99 (9%)
Query: 697 TSVKPSKIIDHFERKFLKELEVAIAK---RAAQGLKNM-NIEQSRDQMEDDVEDDEGEGA 752
T V + + + K KE+ A G +N N Q D ++ E+ + +
Sbjct: 3 TKVDAAAELSAKDLKEKKEVVEEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDE 62
Query: 753 EGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFE 791
E G + E +EE + K+ ++E++D E
Sbjct: 63 EEEGE-----GEEEEGEEEEETEGATGKRAAEDEEDDAE 96
>gnl|CDD|218673 pfam05642, Sporozoite_P67, Sporozoite P67 surface antigen. This
family consists of several Theileria P67 surface
antigens. A stage specific surface antigen of Theileria
parva, p67, is the basis for the development of an
anti-sporozoite vaccine for the control of East Coast
fever (ECF) in cattle. The antigen has been shown to
contain five distinct linear peptide sequences
recognised by sporozoite-neutralising murine monoclonal
antibodies.
Length = 727
Score = 31.2 bits (70), Expect = 3.8
Identities = 13/50 (26%), Positives = 26/50 (52%)
Query: 765 SSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSNIGER 814
S E +E VQ + + NQ+ + E+++ SE E++ +TS+ +
Sbjct: 88 SFQEPVSQESEVQDNTEQNQDTKGSKTDSEEDDDDSEEEDNKSTSSKDGK 137
>gnl|CDD|227458 COG5129, MAK16, Nuclear protein with HMG-like acidic region
[General function prediction only].
Length = 303
Score = 30.8 bits (69), Expect = 3.8
Identities = 31/140 (22%), Positives = 54/140 (38%), Gaps = 17/140 (12%)
Query: 689 PAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNI------------EQS 736
P R+K + + FE+ KEL + K G +N+ E+
Sbjct: 138 PKMNRREKLRERKALNAAKFEKNIEKEL-MLRLKSGIYGDTPLNVREHLWNKAATEREKR 196
Query: 737 RDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDE 796
+D+ E VE++E E D S E+ ++D + E ++ EE E
Sbjct: 197 QDEKERYVEEEEESDTELEAVT----DDSEKEKTKKKDLEKWLGSDQSMETSESEEEESS 252
Query: 797 ERMSEREEDDNTSNIGERFK 816
E S+ +ED++ + K
Sbjct: 253 ESESDEDEDEDNKGKIRKRK 272
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 30.7 bits (69), Expect = 4.0
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 3/77 (3%)
Query: 736 SRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPED 795
+ E D+E ++ G A +VD + EE A + + ++ E E PE
Sbjct: 363 VEETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEP---EVPEK 419
Query: 796 EERMSEREEDDNTSNIG 812
+ + + D + G
Sbjct: 420 AAPIPDPAKPDELAVAG 436
>gnl|CDD|183350 PRK11872, antC, anthranilate dioxygenase reductase; Provisional.
Length = 340
Score = 30.9 bits (70), Expect = 4.1
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 12/64 (18%)
Query: 291 PFPANNLQFMVESGAKGSTVNTMQISCLLGQ-IELEG----------KRPAMMVSGRT-L 338
P N LQF++ G N ++ C +G I E +RP + V+G T L
Sbjct: 162 PNATNQLQFLIRLLPDGVMSNYLRERCQVGDEILFEAPLGAFYLREVERPLVFVAGGTGL 221
Query: 339 PSFL 342
+FL
Sbjct: 222 SAFL 225
>gnl|CDD|176050 cd08405, C2B_Synaptotagmin-7, C2 domain second repeat present in
Synaptotagmin 7. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 7, a member of
class 2 synaptotagmins, is located in presynaptic plasma
membranes in neurons, dense-core vesicles in endocrine
cells, and lysosomes in fibroblasts. It has been shown
to play a role in regulation of Ca2+-dependent lysosomal
exocytosis in fibroblasts and may also function as a
vesicular Ca2+-sensor. It is distinguished from the
other synaptotagmins by having over 12 splice forms.
Previously all synaptotagmins were thought to be calcium
sensors in the regulation of neurotransmitter release
and hormone secretion, but it has been shown that not
all of them bind calcium. Of the 17 identified
synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10).
The function of the two C2 domains that bind calcium
are: regulating the fusion step of synaptic vesicle
exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 29.3 bits (66), Expect = 4.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 946 VAMNRNGIRLNPSFIQKMTFEMPLEKIRQASM 977
V R LNP F + F +PLE++R+ ++
Sbjct: 57 VIKKRT---LNPVFNESFIFNIPLERLRETTL 85
>gnl|CDD|130366 TIGR01299, synapt_SV2, synaptic vesicle protein SV2. This model
describes a tightly conserved subfamily of the larger
family of sugar (and other) transporters described by
PFAM model pfam00083. Members of this subfamily include
closely related forms SV2A and SV2B of synaptic vesicle
protein from vertebrates and a more distantly related
homolog (below trusted cutoff) from Drosophila
melanogaster. Members are predicted to have two sets of
six transmembrane helices.
Length = 742
Score = 31.1 bits (70), Expect = 4.3
Identities = 24/102 (23%), Positives = 43/102 (42%), Gaps = 14/102 (13%)
Query: 693 YRDKTS-VKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQME--DDVEDDEG 749
++D+ + +K +K I KE++ AK+ + L E S+ +D +DD+
Sbjct: 5 FKDRAAFIKGAKDI-------AKEVKKHAAKKVNKALDRAQDEYSQRSYSRFEDEDDDDD 57
Query: 750 EGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFE 791
A G + G +E DA + H E+D +E
Sbjct: 58 FPAPADGYSRGEAADDEEEGEASSDATEGH----DEDDEIYE 95
>gnl|CDD|180766 PRK06940, PRK06940, short chain dehydrogenase; Provisional.
Length = 275
Score = 30.4 bits (69), Expect = 4.5
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 294 ANNLQFMVES---GAKGSTVNTMQ---ISCLLGQIELEGKRPAMM 332
AN L+ M E+ G +G+ +N++ IS L Q EL G R
Sbjct: 175 ANALRVMAEAVKWGERGARINSISPGIISTPLAQDELNGPRGDGY 219
>gnl|CDD|241536 cd13385, PH_Gab3, Grb2-associated binding protein 3 pleckstrin
homology (PH) domain. The Gab subfamily includes
several Gab proteins, Drosophila DOS and C. elegans
SOC-1. They are scaffolding adaptor proteins, which
possess N-terminal PH domains and a C-terminus with
proline-rich regions and multiple phosphorylation sites.
Following activation of growth factor receptors, Gab
proteins are tyrosine phosphorylated and activate PI3K,
which generates 3-phosphoinositide lipids. By binding to
these lipids via the PH domain, Gab proteins remain in
proximity to the receptor, leading to further signaling.
While not all Gab proteins depend on the PH domain for
recruitment, it is required for Gab activity. The
members in this cd include the Gab1, Gab2, and Gab3
proteins. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 125
Score = 29.1 bits (65), Expect = 4.7
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 693 YRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQ 726
YR+K S KP ++ID E + K V K+ Q
Sbjct: 48 YRNKHSKKPIRVIDLNECEVTKHAGVNFIKKEFQ 81
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 30.4 bits (69), Expect = 5.0
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 760 GRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSN 810
G +V +E D E+ ++ ++ +E+D E EDEE E EE+D+
Sbjct: 267 GEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEG 317
>gnl|CDD|173623 cd00180, PKc, Catalytic domain of Protein Kinases. Protein Kinases
(PKs), catalytic (c) domain. PKs catalyze the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The PK family is part of a larger
superfamily that includes the catalytic domains of RIO
kinases, aminoglycoside phosphotransferase, choline
kinase, phosphoinositide 3-kinase (PI3K), and
actin-fragmin kinase. PKs make up a large family of
serine/threonine kinases, protein tyrosine kinases
(PTKs), and dual-specificity PKs that phosphorylate both
serine/threonine and tyrosine residues of target
proteins. Majority of protein phosphorylation, about
95%, occurs on serine residues while only 1% occurs on
tyrosine residues. Protein phosphorylation is a
mechanism by which a wide variety of cellular proteins,
such as enzymes and membrane channels, are reversibly
regulated in response to certain stimuli. PKs often
function as components of signal transduction pathways
in which one kinase activates a second kinase, which in
turn, may act on other kinases; this sequential action
transmits a signal from the cell surface to target
proteins, which results in cellular responses. The PK
family is one of the largest known protein families with
more than 100 homologous yeast enzymes and 550 human
proteins. A fraction of PK family members are
pseudokinases that lack crucial residues for catalytic
activity. The mutiplicity of kinases allows for specific
regulation according to substrate, tissue distribution,
and cellular localization. PKs regulate many cellular
processes including proliferation, division,
differentiation, motility, survival, metabolism,
cell-cycle progression, cytoskeletal rearrangement,
immunity, and neuronal functions. Many kinases are
implicated in the development of various human diseases
including different types of cancer.
Length = 215
Score = 29.9 bits (68), Expect = 5.0
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 910 RVIIREVK--------NVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSFIQ 961
++RE++ N+ +YG+ D HL LV +Y + N +L+ I
Sbjct: 36 EELLREIEILKKLNHPNIVKLYGVFEDENHLYLVMEYCEGGSLKDLLKENEGKLSEDEIL 95
Query: 962 KMTFEM 967
++ ++
Sbjct: 96 RILLQI 101
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit
[Transcription].
Length = 175
Score = 29.3 bits (66), Expect = 6.6
Identities = 18/69 (26%), Positives = 30/69 (43%)
Query: 737 RDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDE 796
++ ++DE + E S D+E D+ED ED++ +E ED+
Sbjct: 106 EVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDD 165
Query: 797 ERMSEREED 805
+ E EED
Sbjct: 166 DEDEEDEED 174
>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional.
Length = 80
Score = 27.8 bits (62), Expect = 6.6
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 4/63 (6%)
Query: 714 KELEVAIAKRAAQGLKNMNIEQSRDQM----EDDVEDDEGEGAEGAGAALGRVDVSSDEE 769
KE + R ++ +E +R M E + +DD+ + + D D+E
Sbjct: 18 KEFASIMEARTEALIEEEKVEIARSVMIEGEEPEDDDDDEDDDDDDDKDDKDDDDDDDDE 77
Query: 770 RDE 772
DE
Sbjct: 78 DDE 80
>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region. The precise
function of this eukaryotic protein family is unknown.
The yeast orthologues have been implicated in cell cycle
progression and biogenesis of 60S ribosomal subunits.
The Schistosoma mansoni Mak16 has been shown to target
protein transport to the nucleolus.
Length = 97
Score = 27.9 bits (62), Expect = 7.6
Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 15/91 (16%)
Query: 694 RDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSR----------DQMEDD 743
R++ ++ +K+ E++ L+ L K+ G + NI QS ++ +++
Sbjct: 12 REEKALVAAKLEKTIEKELLERL-----KQGTYGDEPYNISQSAFKKALEAEESEENDEE 66
Query: 744 VEDDEGEGAEGAGAALGRVDVSSDEERDEED 774
E++E E EG + + +E D ED
Sbjct: 67 EEEEEEEEDEGEIEYVSDDEELEEEIEDLED 97
>gnl|CDD|226907 COG4530, COG4530, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 129
Score = 28.7 bits (64), Expect = 7.8
Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 743 DVEDDEGEGAEGAGAALGRVD-VSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSE 801
E++E E + A V+ VS ++ D+ + +ED D ++ +D+ + +
Sbjct: 49 AAEEEEEEVVKEVDAENEEVEVVSLEDADDDPKGGDDLPDLGDDEDVDLDDDDDDTFLED 108
Query: 802 REEDD 806
E+DD
Sbjct: 109 EEDDD 113
>gnl|CDD|227931 COG5644, COG5644, Uncharacterized conserved protein [Function
unknown].
Length = 869
Score = 30.1 bits (67), Expect = 8.2
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 12/74 (16%)
Query: 760 GRVDVSSDEERDEE---DAVQSHKKVNQEEDNDFEEPEDEERMSERE--------EDDNT 808
D E+ DE+ V S + D F+E EDE+R ++ + +
Sbjct: 29 AGFDSEELEDNDEQGYSFGVNSEDDEEIDSDEAFDE-EDEKRFADWSFNASKSGKSNKDH 87
Query: 809 SNIGERFKIEFRDS 822
N+ +I DS
Sbjct: 88 KNLNNTKEISLNDS 101
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
subunit. The alpha-subunit of the TRAP complex (TRAP
alpha) is a single-spanning membrane protein of the
endoplasmic reticulum (ER) which is found in proximity
of nascent polypeptide chains translocating across the
membrane.
Length = 281
Score = 29.4 bits (66), Expect = 8.4
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 9/55 (16%)
Query: 754 GAGAALGRV--DVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREEDD 806
G G D++ DEE +++ V+++E+++ EDE ++E EED+
Sbjct: 22 GNGKGPFASAQDLTEDEEAEDD-------VVDEDEEDEAVVEEDENELTEEEEDE 69
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation
[Intracellular trafficking and secretion].
Length = 776
Score = 30.0 bits (67), Expect = 8.6
Identities = 24/143 (16%), Positives = 44/143 (30%), Gaps = 15/143 (10%)
Query: 668 KEWLEISPEPHMNYQMKF---CFIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRA 724
L N F+ +M + + +D+ + + R
Sbjct: 276 DVILFEEVRTETNPYFDQKNTTFVWNYMEDNVFHSFSLRFLDNLDFLQFLSKYIGCLWRN 335
Query: 725 AQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQ 784
K N E + +D + D E + + E R+ E+
Sbjct: 336 LNNEKWGNEE---AERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEE---------S 383
Query: 785 EEDNDFEEPEDEERMSEREEDDN 807
E + + E+ EDE S+R DD+
Sbjct: 384 EHEEEVEDYEDENDHSKRICDDD 406
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 29.3 bits (66), Expect = 8.7
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 734 EQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAVQSHKKVNQEEDNDFEEP 793
+ ++V+++E E A DEE +EE+ + EE +D E
Sbjct: 55 DDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEEN------EEEDEESSDENEK 108
Query: 794 EDEERMSEREED 805
E EE+ E
Sbjct: 109 ETEEKTESNVEK 120
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 29.9 bits (67), Expect = 8.9
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 767 DEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREED-DNTSNIGERFKIEFRDSTNV 825
+ E H+K ++ D E ++ M E E+D D+ N + +E ++
Sbjct: 687 NAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEELEALEA 746
Query: 826 FVKD 829
+
Sbjct: 747 NLLA 750
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.1 bits (67), Expect = 9.1
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 5/92 (5%)
Query: 726 QGLKNMNIEQSRDQMEDDVEDDEGEGAEG-AGAALGRVDVSSDEERDEEDAVQSHKKVNQ 784
+GLK + D ED+ D+ E A G A A ++E R E+A + + +
Sbjct: 1070 EGLKPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARK 1129
Query: 785 EEDNDFEEPEDEERMSE--REEDDNTSNIGER 814
E + + ED + E + ED I +
Sbjct: 1130 AE--EARKAEDARKAEEARKAEDAKRVEIARK 1159
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 29.5 bits (66), Expect = 9.4
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 763 DVSSDEERDEEDAVQSHKKVNQEEDNDFEEPEDEERMSEREE 804
D+ E E+ + + +E+++ E DE + E E
Sbjct: 327 DIFEVVEVVEKQEGDVVTEESTDEESEDEVEIDESVIEEVAE 368
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 29.7 bits (67), Expect = 9.7
Identities = 35/154 (22%), Positives = 54/154 (35%), Gaps = 26/154 (16%)
Query: 668 KEWL--EISPE--PHMNYQ-MKFCF------IPAHMYRDKTSVKPSKIIDHFERKFLKEL 716
K WL +SPE P N + + F F A + K + HF+ F + L
Sbjct: 295 KRWLGTPVSPEMNPTFNLENLSFIFNYTTEDGIALSW--LLKFKDADAFTHFQEGFTQAL 352
Query: 717 EVAIAKRAAQGLKNMNIEQSRDQMEDDVEDDEGEGAEGAGAALGRVDVSSDEERDEEDAV 776
+ K+ K E +D + D E E A D +EE DE++
Sbjct: 353 WETLNKQKWTKAK----ETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGP 408
Query: 777 QSHKKVNQEEDNDFEEPEDEERMSEREEDDNTSN 810
++ E EE E + +D+ N
Sbjct: 409 SKEH---------SDDEEFEEDDVESKYEDSDGN 433
>gnl|CDD|129416 TIGR00316, cdhC, CO dehydrogenase/CO-methylating acetyl-CoA
synthase complex, beta subunit. Nomenclature follows
the description for Methanosarcina thermophila. The
CO-methylating acetyl-CoA synthase is considered the
defining enzyme of the Wood-Ljungdahl pathway, used for
acetate catabolism by sulfate reducing bacteria but for
acetate biosynthesis by acetogenic bacteria such as
oorella thermoacetica (f. Clostridium thermoaceticum)
[Energy metabolism, Chemoautotrophy].
Length = 458
Score = 29.4 bits (66), Expect = 9.8
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 687 FIPAHMYRDKTSVKPSKIIDHFERKFLKELEVAIAKRAAQGLKNMNIEQSRDQMEDDVED 746
IP + + + +K D RKFLKE + KR + + IE+ ++ E+
Sbjct: 363 AIPEDLRDKIATEEDAKTTDEL-RKFLKEKGHPVVKRVVREVDEEEIEE--EEEAMQPEE 419
Query: 747 DEGEGAE 753
E EG E
Sbjct: 420 MEMEGFE 426
>gnl|CDD|214567 smart00220, S_TKc, Serine/Threonine protein kinases, catalytic
domain. Phosphotransferases. Serine or
threonine-specific kinase subfamily.
Length = 254
Score = 29.4 bits (67), Expect = 9.8
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 912 IIREVK--------NVFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNPSFIQKM 963
I+RE+K N+ +Y + D L LV +Y + + + G RL+ +
Sbjct: 44 ILREIKILKKLKHPNIVRLYDVFEDEDKLYLVMEYCEGGDLFDLLKKRG-RLSEDEARFY 102
Query: 964 TFEM 967
++
Sbjct: 103 LRQI 106
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.394
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 52,304,640
Number of extensions: 5291087
Number of successful extensions: 6150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5703
Number of HSP's successfully gapped: 192
Length of query: 1020
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 913
Effective length of database: 6,191,724
Effective search space: 5653044012
Effective search space used: 5653044012
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 64 (28.3 bits)